[9ff861b] | 1 | """ |
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| 2 | This software was developed by the University of Tennessee as part of the |
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| 3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 4 | project funded by the US National Science Foundation. |
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| 5 | |
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| 6 | See the license text in license.txt |
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| 7 | |
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| 8 | copyright 2009, University of Tennessee |
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| 9 | """ |
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| 10 | |
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[f3d51f6] | 11 | # Make sure the option of saving each curve is available |
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| 12 | # Use the I(q) curve as input and compare the output to P(r) |
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| 13 | |
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| 14 | import os |
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[4a5de6f] | 15 | import sys |
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[f3d51f6] | 16 | import wx |
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[aa4b8379] | 17 | import logging |
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[302510b] | 18 | import time |
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[0d88a09] | 19 | from sans.guiframe.dataFitting import Data1D |
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| 20 | from danse.common.plottools import Theory1D |
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[f3d51f6] | 21 | from sans.guicomm.events import NewPlotEvent, StatusEvent |
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| 22 | import math, numpy |
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| 23 | from sans.pr.invertor import Invertor |
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[aab8ad7] | 24 | from DataLoader.loader import Loader |
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[d7412e0] | 25 | from sans.guiframe.data_loader import load_error |
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[f3d51f6] | 26 | |
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[0d88a09] | 27 | import copy |
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| 28 | |
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[f1181977] | 29 | PR_FIT_LABEL = r"$P_{fit}(r)$" |
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| 30 | PR_LOADED_LABEL = r"$P_{loaded}(r)$" |
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| 31 | IQ_DATA_LABEL = r"$I_{obs}(q)$" |
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| 32 | IQ_FIT_LABEL = r"$I_{fit}(q)$" |
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| 33 | IQ_SMEARED_LABEL = r"$I_{smeared}(q)$" |
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[aa4b8379] | 34 | |
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| 35 | import wx.lib |
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| 36 | (NewPrFileEvent, EVT_PR_FILE) = wx.lib.newevent.NewEvent() |
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| 37 | |
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| 38 | |
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[f3d51f6] | 39 | class Plugin: |
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| 40 | |
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[b659551] | 41 | DEFAULT_ALPHA = 0.0001 |
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| 42 | DEFAULT_NFUNC = 10 |
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| 43 | DEFAULT_DMAX = 140.0 |
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| 44 | |
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[d2ee6f6] | 45 | def __init__(self, standalone=True): |
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[f3d51f6] | 46 | ## Plug-in name |
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| 47 | self.sub_menu = "Pr inversion" |
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| 48 | |
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| 49 | ## Reference to the parent window |
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| 50 | self.parent = None |
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| 51 | |
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| 52 | ## Simulation window manager |
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| 53 | self.simview = None |
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| 54 | |
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| 55 | ## List of panels for the simulation perspective (names) |
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| 56 | self.perspective = [] |
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| 57 | |
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| 58 | ## State data |
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[b659551] | 59 | self.alpha = self.DEFAULT_ALPHA |
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| 60 | self.nfunc = self.DEFAULT_NFUNC |
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| 61 | self.max_length = self.DEFAULT_DMAX |
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[634f1cf] | 62 | self.q_min = None |
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| 63 | self.q_max = None |
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[a4bd2ac] | 64 | self.has_bck = False |
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[2a92852] | 65 | self.slit_height = 0 |
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| 66 | self.slit_width = 0 |
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[f3d51f6] | 67 | ## Remember last plottable processed |
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| 68 | self.last_data = "sphere_60_q0_2.txt" |
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[0bae207] | 69 | self._current_file_data = None |
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[f3d51f6] | 70 | ## Time elapsed for last computation [sec] |
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| 71 | # Start with a good default |
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| 72 | self.elapsed = 0.022 |
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[aa4b8379] | 73 | self.iq_data_shown = False |
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[f3d51f6] | 74 | |
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| 75 | ## Current invertor |
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| 76 | self.invertor = None |
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[3fd1ebc] | 77 | self.pr = None |
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[feb21d8] | 78 | # Copy of the last result in case we need to display it. |
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| 79 | self._last_pr = None |
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| 80 | self._last_out = None |
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| 81 | self._last_cov = None |
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[f3d51f6] | 82 | ## Calculation thread |
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| 83 | self.calc_thread = None |
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| 84 | ## Estimation thread |
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| 85 | self.estimation_thread = None |
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| 86 | ## Result panel |
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| 87 | self.control_panel = None |
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| 88 | ## Currently views plottable |
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| 89 | self.current_plottable = None |
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[b659551] | 90 | ## Number of P(r) points to display on the output plot |
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| 91 | self._pr_npts = 51 |
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[aa4b8379] | 92 | ## Flag to let the plug-in know that it is running standalone |
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[d2ee6f6] | 93 | self.standalone = standalone |
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[feb21d8] | 94 | self._normalize_output = False |
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| 95 | self._scale_output_unity = False |
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[aa4b8379] | 96 | |
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[f1181977] | 97 | ## List of added P(r) plots |
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| 98 | self._added_plots = {} |
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| 99 | self._default_Iq = {} |
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| 100 | |
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[6f1f129] | 101 | # Associate the inversion state reader with .prv files |
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| 102 | from DataLoader.loader import Loader |
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| 103 | from inversion_state import Reader |
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| 104 | |
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[0d88a09] | 105 | # Create a CanSAS/Pr reader |
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| 106 | self.state_reader = Reader(self.set_state) |
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[6f1f129] | 107 | l = Loader() |
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[410aad8] | 108 | l.associate_file_reader('.prv', self.state_reader) |
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[6f1f129] | 109 | |
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[aa4b8379] | 110 | # Log startup |
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| 111 | logging.info("Pr(r) plug-in started") |
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| 112 | |
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[410aad8] | 113 | def set_state(self, state, datainfo=None): |
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[6f1f129] | 114 | """ |
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| 115 | Call-back method for the inversion state reader. |
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| 116 | This method is called when a .prv file is loaded. |
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| 117 | |
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| 118 | @param state: InversionState object |
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[410aad8] | 119 | @param datainfo: Data1D object [optional] |
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[6f1f129] | 120 | """ |
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[410aad8] | 121 | try: |
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[0d88a09] | 122 | if datainfo is None: |
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| 123 | raise RuntimeError, "Pr.set_state: datainfo parameter cannot be None in standalone mode" |
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[302510b] | 124 | |
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[0d88a09] | 125 | # Ensuring that plots are coordinated correctly |
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| 126 | t = time.localtime(datainfo.meta_data['prstate'].timestamp) |
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| 127 | time_str = time.strftime("%b %d %H:%M", t) |
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| 128 | |
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| 129 | # Check that no time stamp is already appended |
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| 130 | max_char = datainfo.meta_data['prstate'].file.find("[") |
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| 131 | if max_char < 0: |
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| 132 | max_char = len(datainfo.meta_data['prstate'].file) |
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| 133 | |
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| 134 | datainfo.meta_data['prstate'].file = datainfo.meta_data['prstate'].file[0:max_char] +' [' + time_str + ']' |
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| 135 | datainfo.filename = datainfo.meta_data['prstate'].file |
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[410aad8] | 136 | |
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[0d88a09] | 137 | self.current_plottable = datainfo |
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| 138 | self.current_plottable.group_id = datainfo.meta_data['prstate'].file |
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| 139 | |
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[410aad8] | 140 | # Load the P(r) results |
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| 141 | self.control_panel.set_state(state) |
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| 142 | |
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| 143 | # Make sure the user sees the P(r) panel after loading |
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| 144 | self.parent.set_perspective(self.perspective) |
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| 145 | |
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| 146 | except: |
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| 147 | logging.error("prview.set_state: %s" % sys.exc_value) |
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[f3d51f6] | 148 | |
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| 149 | def populate_menu(self, id, owner): |
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| 150 | """ |
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| 151 | Create a menu for the plug-in |
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| 152 | """ |
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[7cb0353] | 153 | return [] |
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[f3d51f6] | 154 | |
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[119a11d] | 155 | def help(self, evt): |
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| 156 | """ |
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| 157 | Show a general help dialog. |
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| 158 | TODO: replace the text with a nice image |
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| 159 | """ |
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| 160 | from inversion_panel import HelpDialog |
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| 161 | dialog = HelpDialog(None, -1) |
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| 162 | if dialog.ShowModal() == wx.ID_OK: |
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| 163 | dialog.Destroy() |
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| 164 | else: |
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| 165 | dialog.Destroy() |
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| 166 | |
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[f3d51f6] | 167 | def _fit_pr(self, evt): |
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| 168 | from sans.pr.invertor import Invertor |
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| 169 | import numpy |
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| 170 | import pylab |
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| 171 | import math |
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| 172 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 173 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 174 | |
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| 175 | # Generate P(r) for sphere |
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| 176 | radius = 60.0 |
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| 177 | d_max = 2*radius |
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| 178 | |
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| 179 | |
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| 180 | r = pylab.arange(0.01, d_max, d_max/51.0) |
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| 181 | M = len(r) |
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| 182 | y = numpy.zeros(M) |
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| 183 | pr_err = numpy.zeros(M) |
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| 184 | |
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| 185 | sum = 0.0 |
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| 186 | for j in range(M): |
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| 187 | value = self.pr_theory(r[j], radius) |
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| 188 | sum += value |
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| 189 | y[j] = value |
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| 190 | pr_err[j] = math.sqrt(y[j]) |
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| 191 | |
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| 192 | |
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| 193 | y = y/sum*d_max/len(r) |
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| 194 | |
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| 195 | |
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| 196 | |
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| 197 | # Perform fit |
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| 198 | pr = Invertor() |
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| 199 | pr.d_max = d_max |
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| 200 | pr.alpha = 0 |
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| 201 | pr.x = r |
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| 202 | pr.y = y |
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| 203 | pr.err = pr_err |
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| 204 | out, cov = pr.pr_fit() |
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| 205 | for i in range(len(out)): |
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| 206 | print "%g +- %g" % (out[i], math.sqrt(cov[i][i])) |
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| 207 | |
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| 208 | |
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| 209 | # Show input P(r) |
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[b659551] | 210 | new_plot = Data1D(pr.x, pr.y, dy=pr.err) |
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[f3d51f6] | 211 | new_plot.name = "P_{obs}(r)" |
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| 212 | new_plot.xaxis("\\rm{r}", 'A') |
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| 213 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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| 214 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Pr")) |
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| 215 | |
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| 216 | # Show P(r) fit |
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| 217 | self.show_pr(out, pr) |
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| 218 | |
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| 219 | # Show I(q) fit |
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| 220 | q = pylab.arange(0.001, 0.1, 0.01/51.0) |
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| 221 | self.show_iq(out, pr, q) |
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| 222 | |
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| 223 | |
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| 224 | def show_shpere(self, x, radius=70.0, x_range=70.0): |
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| 225 | import numpy |
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| 226 | import pylab |
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| 227 | import math |
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| 228 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 229 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 230 | # Show P(r) |
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| 231 | y_true = numpy.zeros(len(x)) |
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| 232 | |
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| 233 | sum_true = 0.0 |
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| 234 | for i in range(len(x)): |
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| 235 | y_true[i] = self.pr_theory(x[i], radius) |
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| 236 | sum_true += y_true[i] |
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| 237 | |
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| 238 | y_true = y_true/sum_true*x_range/len(x) |
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| 239 | |
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| 240 | # Show the theory P(r) |
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| 241 | new_plot = Theory1D(x, y_true) |
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| 242 | new_plot.name = "P_{true}(r)" |
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| 243 | new_plot.xaxis("\\rm{r}", 'A') |
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| 244 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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| 245 | |
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| 246 | |
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| 247 | #Put this call in plottables/guitools |
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| 248 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Sphere P(r)")) |
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| 249 | |
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[b659551] | 250 | def get_npts(self): |
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| 251 | """ |
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| 252 | Returns the number of points in the I(q) data |
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| 253 | """ |
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| 254 | try: |
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| 255 | return len(self.pr.x) |
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| 256 | except: |
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| 257 | return 0 |
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| 258 | |
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[f3d51f6] | 259 | def show_iq(self, out, pr, q=None): |
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| 260 | import numpy |
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| 261 | import pylab |
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| 262 | import math |
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| 263 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 264 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 265 | |
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| 266 | qtemp = pr.x |
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| 267 | if not q==None: |
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| 268 | qtemp = q |
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| 269 | |
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| 270 | # Make a plot |
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| 271 | maxq = -1 |
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| 272 | for q_i in qtemp: |
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| 273 | if q_i>maxq: |
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| 274 | maxq=q_i |
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| 275 | |
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[634f1cf] | 276 | minq = 0.001 |
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| 277 | |
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| 278 | # Check for user min/max |
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| 279 | if not pr.q_min==None: |
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| 280 | minq = pr.q_min |
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| 281 | if not pr.q_max==None: |
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| 282 | maxq = pr.q_max |
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| 283 | |
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| 284 | x = pylab.arange(minq, maxq, maxq/301.0) |
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[f3d51f6] | 285 | y = numpy.zeros(len(x)) |
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| 286 | err = numpy.zeros(len(x)) |
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| 287 | for i in range(len(x)): |
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| 288 | value = pr.iq(out, x[i]) |
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| 289 | y[i] = value |
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| 290 | try: |
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| 291 | err[i] = math.sqrt(math.fabs(value)) |
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| 292 | except: |
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| 293 | err[i] = 1.0 |
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| 294 | print "Error getting error", value, x[i] |
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| 295 | |
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| 296 | new_plot = Theory1D(x, y) |
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[2a92852] | 297 | new_plot.name = IQ_FIT_LABEL |
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[f3d51f6] | 298 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 299 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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[d2ee6f6] | 300 | |
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| 301 | title = "I(q)" |
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| 302 | # If we have a group ID, use it |
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| 303 | if pr.info.has_key("plot_group_id"): |
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| 304 | new_plot.group_id = pr.info["plot_group_id"] |
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| 305 | title = pr.info["plot_group_id"] |
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| 306 | |
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| 307 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=title)) |
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[f3d51f6] | 308 | |
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[2a92852] | 309 | # If we have used slit smearing, plot the smeared I(q) too |
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| 310 | if pr.slit_width>0 or pr.slit_height>0: |
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| 311 | x = pylab.arange(minq, maxq, maxq/301.0) |
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| 312 | y = numpy.zeros(len(x)) |
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| 313 | err = numpy.zeros(len(x)) |
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| 314 | for i in range(len(x)): |
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| 315 | value = pr.iq_smeared(out, x[i]) |
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| 316 | y[i] = value |
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| 317 | try: |
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| 318 | err[i] = math.sqrt(math.fabs(value)) |
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| 319 | except: |
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| 320 | err[i] = 1.0 |
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| 321 | print "Error getting error", value, x[i] |
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| 322 | |
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| 323 | new_plot = Theory1D(x, y) |
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| 324 | new_plot.name = IQ_SMEARED_LABEL |
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| 325 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
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| 326 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
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| 327 | #new_plot.group_id = "test group" |
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| 328 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="I(q)")) |
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| 329 | |
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[f3d51f6] | 330 | |
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[b659551] | 331 | def _on_pr_npts(self, evt): |
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| 332 | """ |
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| 333 | Redisplay P(r) with a different number of points |
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| 334 | """ |
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| 335 | from inversion_panel import PrDistDialog |
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| 336 | dialog = PrDistDialog(None, -1) |
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| 337 | dialog.set_content(self._pr_npts) |
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| 338 | if dialog.ShowModal() == wx.ID_OK: |
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| 339 | self._pr_npts= dialog.get_content() |
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| 340 | dialog.Destroy() |
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[feb21d8] | 341 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
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[b659551] | 342 | else: |
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| 343 | dialog.Destroy() |
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[f3d51f6] | 344 | |
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| 345 | |
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| 346 | def show_pr(self, out, pr, cov=None): |
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| 347 | import numpy |
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| 348 | import pylab |
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| 349 | import math |
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| 350 | from sans.guicomm.events import NewPlotEvent |
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[ff7acff] | 351 | from danse.common.plottools import Data1D, Theory1D |
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[f3d51f6] | 352 | |
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| 353 | # Show P(r) |
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[b659551] | 354 | x = pylab.arange(0.0, pr.d_max, pr.d_max/self._pr_npts) |
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[f3d51f6] | 355 | |
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| 356 | y = numpy.zeros(len(x)) |
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| 357 | dy = numpy.zeros(len(x)) |
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| 358 | y_true = numpy.zeros(len(x)) |
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| 359 | |
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| 360 | sum = 0.0 |
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[feb21d8] | 361 | pmax = 0.0 |
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[dfb58f8] | 362 | cov2 = numpy.ascontiguousarray(cov) |
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| 363 | |
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[f3d51f6] | 364 | for i in range(len(x)): |
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[dfb58f8] | 365 | if cov2==None: |
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[f3d51f6] | 366 | value = pr.pr(out, x[i]) |
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| 367 | else: |
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[dfb58f8] | 368 | (value, dy[i]) = pr.pr_err(out, cov2, x[i]) |
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[660b1e6] | 369 | sum += value*pr.d_max/len(x) |
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[f3d51f6] | 370 | |
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[feb21d8] | 371 | # keep track of the maximum P(r) value |
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| 372 | if value>pmax: |
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| 373 | pmax = value |
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| 374 | |
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| 375 | y[i] = value |
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| 376 | |
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| 377 | if self._normalize_output==True: |
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| 378 | y = y/sum |
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| 379 | dy = dy/sum |
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| 380 | elif self._scale_output_unity==True: |
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| 381 | y = y/pmax |
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| 382 | dy = dy/pmax |
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[f3d51f6] | 383 | |
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[dfb58f8] | 384 | if cov2==None: |
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[f3d51f6] | 385 | new_plot = Theory1D(x, y) |
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| 386 | else: |
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| 387 | new_plot = Data1D(x, y, dy=dy) |
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[f1181977] | 388 | new_plot.name = PR_FIT_LABEL |
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[f3d51f6] | 389 | new_plot.xaxis("\\rm{r}", 'A') |
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| 390 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
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[d2ee6f6] | 391 | # Make sure that the plot is linear |
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| 392 | new_plot.xtransform="x" |
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| 393 | new_plot.ytransform="y" |
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[f3d51f6] | 394 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="P(r) fit")) |
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| 395 | |
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| 396 | return x, pr.d_max |
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| 397 | |
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| 398 | |
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[6f1f129] | 399 | def choose_file(self, path=None): |
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[f3d51f6] | 400 | """ |
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| 401 | |
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| 402 | """ |
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| 403 | #TODO: this should be in a common module |
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[6f1f129] | 404 | return self.parent.choose_file(path=path) |
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[f3d51f6] | 405 | |
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[0bae207] | 406 | |
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| 407 | def load(self, path): |
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| 408 | """ |
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| 409 | Load data. This will eventually be replaced |
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| 410 | by our standard DataLoader class. |
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| 411 | """ |
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| 412 | class FileData: |
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| 413 | x = None |
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| 414 | y = None |
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| 415 | err = None |
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| 416 | path = None |
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| 417 | |
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| 418 | def __init__(self, path): |
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| 419 | self.path = path |
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| 420 | |
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| 421 | self._current_file_data = FileData(path) |
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| 422 | |
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[aab8ad7] | 423 | # Use data loader to load file |
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| 424 | dataread = Loader().load(path) |
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[ceaf16e] | 425 | |
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| 426 | # Notify the user if we could not read the file |
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| 427 | if dataread is None: |
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| 428 | raise RuntimeError, "Invalid data" |
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| 429 | |
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[aab8ad7] | 430 | x = None |
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| 431 | y = None |
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| 432 | err = None |
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| 433 | if dataread.__class__.__name__ == 'Data1D': |
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| 434 | x = dataread.x |
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| 435 | y = dataread.y |
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| 436 | err = dataread.dy |
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| 437 | else: |
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[e43c012] | 438 | if isinstance(dataread, list) and len(dataread)>0: |
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| 439 | x = dataread[0].x |
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| 440 | y = dataread[0].y |
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| 441 | err = dataread[0].dy |
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| 442 | msg = "PrView only allows a single data set at a time. " |
---|
| 443 | msg += "Only the first data set was loaded." |
---|
| 444 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 445 | else: |
---|
[6f1f129] | 446 | if dataread is None: |
---|
| 447 | return x, y, err |
---|
[e43c012] | 448 | raise RuntimeError, "This tool can only read 1D data" |
---|
[aab8ad7] | 449 | |
---|
[0bae207] | 450 | self._current_file_data.x = x |
---|
| 451 | self._current_file_data.y = y |
---|
| 452 | self._current_file_data.err = err |
---|
| 453 | return x, y, err |
---|
| 454 | |
---|
| 455 | def load_columns(self, path = "sphere_60_q0_2.txt"): |
---|
| 456 | """ |
---|
| 457 | Load 2- or 3- column ascii |
---|
| 458 | """ |
---|
[f3d51f6] | 459 | import numpy, math, sys |
---|
| 460 | # Read the data from the data file |
---|
| 461 | data_x = numpy.zeros(0) |
---|
| 462 | data_y = numpy.zeros(0) |
---|
| 463 | data_err = numpy.zeros(0) |
---|
[b659551] | 464 | scale = None |
---|
| 465 | min_err = 0.0 |
---|
[f3d51f6] | 466 | if not path == None: |
---|
| 467 | input_f = open(path,'r') |
---|
| 468 | buff = input_f.read() |
---|
| 469 | lines = buff.split('\n') |
---|
| 470 | for line in lines: |
---|
| 471 | try: |
---|
| 472 | toks = line.split() |
---|
| 473 | x = float(toks[0]) |
---|
| 474 | y = float(toks[1]) |
---|
[b659551] | 475 | if len(toks)>2: |
---|
| 476 | err = float(toks[2]) |
---|
| 477 | else: |
---|
| 478 | if scale==None: |
---|
| 479 | scale = 0.05*math.sqrt(y) |
---|
| 480 | #scale = 0.05/math.sqrt(y) |
---|
| 481 | min_err = 0.01*y |
---|
| 482 | err = scale*math.sqrt(y)+min_err |
---|
| 483 | #err = 0 |
---|
| 484 | |
---|
[4a5de6f] | 485 | data_x = numpy.append(data_x, x) |
---|
| 486 | data_y = numpy.append(data_y, y) |
---|
[b659551] | 487 | data_err = numpy.append(data_err, err) |
---|
[f3d51f6] | 488 | except: |
---|
[b659551] | 489 | pass |
---|
[f3d51f6] | 490 | |
---|
[357b79b] | 491 | if not scale==None: |
---|
| 492 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 493 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 494 | else: |
---|
| 495 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 496 | |
---|
[b659551] | 497 | return data_x, data_y, data_err |
---|
[f3d51f6] | 498 | |
---|
[0bae207] | 499 | def load_abs(self, path): |
---|
| 500 | """ |
---|
| 501 | Load an IGOR .ABS reduced file |
---|
| 502 | @param path: file path |
---|
| 503 | @return: x, y, err vectors |
---|
| 504 | """ |
---|
| 505 | import numpy, math, sys |
---|
| 506 | # Read the data from the data file |
---|
| 507 | data_x = numpy.zeros(0) |
---|
| 508 | data_y = numpy.zeros(0) |
---|
| 509 | data_err = numpy.zeros(0) |
---|
| 510 | scale = None |
---|
| 511 | min_err = 0.0 |
---|
| 512 | |
---|
| 513 | data_started = False |
---|
| 514 | if not path == None: |
---|
| 515 | input_f = open(path,'r') |
---|
| 516 | buff = input_f.read() |
---|
| 517 | lines = buff.split('\n') |
---|
| 518 | for line in lines: |
---|
| 519 | if data_started==True: |
---|
| 520 | try: |
---|
| 521 | toks = line.split() |
---|
| 522 | x = float(toks[0]) |
---|
| 523 | y = float(toks[1]) |
---|
| 524 | if len(toks)>2: |
---|
| 525 | err = float(toks[2]) |
---|
| 526 | else: |
---|
| 527 | if scale==None: |
---|
| 528 | scale = 0.05*math.sqrt(y) |
---|
| 529 | #scale = 0.05/math.sqrt(y) |
---|
| 530 | min_err = 0.01*y |
---|
| 531 | err = scale*math.sqrt(y)+min_err |
---|
| 532 | #err = 0 |
---|
| 533 | |
---|
| 534 | data_x = numpy.append(data_x, x) |
---|
| 535 | data_y = numpy.append(data_y, y) |
---|
| 536 | data_err = numpy.append(data_err, err) |
---|
| 537 | except: |
---|
| 538 | pass |
---|
| 539 | elif line.find("The 6 columns")>=0: |
---|
| 540 | data_started = True |
---|
| 541 | |
---|
| 542 | if not scale==None: |
---|
| 543 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 544 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 545 | else: |
---|
| 546 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
| 547 | |
---|
| 548 | return data_x, data_y, data_err |
---|
| 549 | |
---|
| 550 | |
---|
| 551 | |
---|
[f3d51f6] | 552 | def pr_theory(self, r, R): |
---|
| 553 | """ |
---|
| 554 | |
---|
| 555 | """ |
---|
| 556 | if r<=2*R: |
---|
| 557 | return 12.0* ((0.5*r/R)**2) * ((1.0-0.5*r/R)**2) * ( 2.0 + 0.5*r/R ) |
---|
| 558 | else: |
---|
| 559 | return 0.0 |
---|
| 560 | |
---|
[660b1e6] | 561 | def get_context_menu(self, graph=None): |
---|
[f3d51f6] | 562 | """ |
---|
| 563 | Get the context menu items available for P(r) |
---|
[660b1e6] | 564 | @param graph: the Graph object to which we attach the context menu |
---|
[f3d51f6] | 565 | @return: a list of menu items with call-back function |
---|
| 566 | """ |
---|
[660b1e6] | 567 | # Look whether this Graph contains P(r) data |
---|
[aa4b8379] | 568 | #if graph.selected_plottable==IQ_DATA_LABEL: |
---|
[660b1e6] | 569 | for item in graph.plottables: |
---|
[aa4b8379] | 570 | if item.name==PR_FIT_LABEL: |
---|
[feb21d8] | 571 | m_list = [["Add P(r) data", "Load a data file and display it on this plot", self._on_add_data], |
---|
[b659551] | 572 | ["Change number of P(r) points", "Change the number of points on the P(r) output", self._on_pr_npts]] |
---|
[aa4b8379] | 573 | |
---|
[900c787] | 574 | if self._scale_output_unity==True or self._normalize_output==True: |
---|
| 575 | m_list.append(["Disable P(r) scaling", |
---|
| 576 | "Let the output P(r) keep the scale of the data", |
---|
| 577 | self._on_disable_scaling]) |
---|
[feb21d8] | 578 | |
---|
| 579 | if self._scale_output_unity==False: |
---|
| 580 | m_list.append(["Scale P_max(r) to unity", |
---|
| 581 | "Scale P(r) so that its maximum is 1", |
---|
| 582 | self._on_scale_unity]) |
---|
| 583 | |
---|
| 584 | if self._normalize_output==False: |
---|
| 585 | m_list.append(["Normalize P(r) to unity", |
---|
| 586 | "Normalize the integral of P(r) to 1", |
---|
| 587 | self._on_normalize]) |
---|
| 588 | |
---|
| 589 | return m_list |
---|
| 590 | #return [["Add P(r) data", "Load a data file and display it on this plot", self._on_add_data], |
---|
| 591 | # ["Change number of P(r) points", "Change the number of points on the P(r) output", self._on_pr_npts]] |
---|
| 592 | |
---|
[aa4b8379] | 593 | elif item.name==graph.selected_plottable: |
---|
[d2ee6f6] | 594 | #TODO: we might want to check that the units are consistent with I(q) |
---|
| 595 | # before allowing this menu item |
---|
[aa4b8379] | 596 | return [["Compute P(r)", "Compute P(r) from distribution", self._on_context_inversion]] |
---|
[660b1e6] | 597 | |
---|
[aa4b8379] | 598 | return [] |
---|
[660b1e6] | 599 | |
---|
[feb21d8] | 600 | def _on_disable_scaling(self, evt): |
---|
| 601 | """ |
---|
| 602 | Disable P(r) scaling |
---|
| 603 | @param evt: Menu event |
---|
| 604 | """ |
---|
| 605 | self._normalize_output = False |
---|
| 606 | self._scale_output_unity = False |
---|
| 607 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 608 | |
---|
[f1181977] | 609 | # Now replot the original added data |
---|
| 610 | for plot in self._added_plots: |
---|
| 611 | self._added_plots[plot].y = numpy.copy(self._default_Iq[plot]) |
---|
| 612 | wx.PostEvent(self.parent, NewPlotEvent(plot=self._added_plots[plot], |
---|
| 613 | title=self._added_plots[plot].name, |
---|
| 614 | update=True)) |
---|
| 615 | |
---|
| 616 | # Need the update flag in the NewPlotEvent to protect against |
---|
| 617 | # the plot no longer being there... |
---|
| 618 | |
---|
[feb21d8] | 619 | def _on_normalize(self, evt): |
---|
| 620 | """ |
---|
[f1181977] | 621 | Normalize the area under the P(r) curve to 1. |
---|
| 622 | This operation is done for all displayed plots. |
---|
| 623 | |
---|
[feb21d8] | 624 | @param evt: Menu event |
---|
| 625 | """ |
---|
| 626 | self._normalize_output = True |
---|
| 627 | self._scale_output_unity = False |
---|
| 628 | |
---|
| 629 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 630 | |
---|
[f1181977] | 631 | # Now scale the added plots too |
---|
| 632 | for plot in self._added_plots: |
---|
| 633 | sum = numpy.sum(self._added_plots[plot].y) |
---|
| 634 | npts = len(self._added_plots[plot].x) |
---|
| 635 | sum *= self._added_plots[plot].x[npts-1]/npts |
---|
| 636 | y = self._added_plots[plot].y/sum |
---|
| 637 | |
---|
| 638 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 639 | new_plot.name = self._added_plots[plot].name |
---|
| 640 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 641 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 642 | |
---|
| 643 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, update=True, |
---|
| 644 | title=self._added_plots[plot].name)) |
---|
| 645 | |
---|
| 646 | |
---|
| 647 | |
---|
[feb21d8] | 648 | def _on_scale_unity(self, evt): |
---|
| 649 | """ |
---|
[f1181977] | 650 | Scale the maximum P(r) value on each displayed plot to 1. |
---|
| 651 | |
---|
[feb21d8] | 652 | @param evt: Menu event |
---|
| 653 | """ |
---|
| 654 | self._scale_output_unity = True |
---|
| 655 | self._normalize_output = False |
---|
| 656 | |
---|
| 657 | self.show_pr(self._last_out, self._last_pr, self._last_cov) |
---|
| 658 | |
---|
[f1181977] | 659 | # Now scale the added plots too |
---|
| 660 | for plot in self._added_plots: |
---|
| 661 | _max = 0 |
---|
| 662 | for y in self._added_plots[plot].y: |
---|
| 663 | if y>_max: |
---|
| 664 | _max = y |
---|
| 665 | y = self._added_plots[plot].y/_max |
---|
| 666 | |
---|
| 667 | new_plot = Theory1D(self._added_plots[plot].x, y) |
---|
| 668 | new_plot.name = self._added_plots[plot].name |
---|
| 669 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 670 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 671 | |
---|
| 672 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, update=True, |
---|
| 673 | title=self._added_plots[plot].name)) |
---|
| 674 | |
---|
| 675 | |
---|
[660b1e6] | 676 | def _on_add_data(self, evt): |
---|
| 677 | """ |
---|
| 678 | Add a data curve to the plot |
---|
| 679 | WARNING: this will be removed once guiframe.plotting has its full functionality |
---|
| 680 | """ |
---|
| 681 | path = self.choose_file() |
---|
| 682 | if path==None: |
---|
| 683 | return |
---|
| 684 | |
---|
[14d05ba] | 685 | #x, y, err = self.parent.load_ascii_1D(path) |
---|
| 686 | # Use data loader to load file |
---|
| 687 | try: |
---|
| 688 | dataread = Loader().load(path) |
---|
| 689 | x = None |
---|
| 690 | y = None |
---|
| 691 | err = None |
---|
| 692 | if dataread.__class__.__name__ == 'Data1D': |
---|
| 693 | x = dataread.x |
---|
| 694 | y = dataread.y |
---|
| 695 | err = dataread.dy |
---|
| 696 | else: |
---|
[e43c012] | 697 | if isinstance(dataread, list) and len(dataread)>0: |
---|
| 698 | x = dataread[0].x |
---|
| 699 | y = dataread[0].y |
---|
| 700 | err = dataread[0].dy |
---|
| 701 | msg = "PrView only allows a single data set at a time. " |
---|
| 702 | msg += "Only the first data set was loaded." |
---|
| 703 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 704 | else: |
---|
| 705 | wx.PostEvent(self.parent, StatusEvent(status="This tool can only read 1D data")) |
---|
| 706 | return |
---|
| 707 | |
---|
[14d05ba] | 708 | except: |
---|
| 709 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 710 | return |
---|
[660b1e6] | 711 | |
---|
[f1181977] | 712 | filename = os.path.basename(path) |
---|
| 713 | |
---|
[b659551] | 714 | #new_plot = Data1D(x, y, dy=err) |
---|
| 715 | new_plot = Theory1D(x, y) |
---|
[f1181977] | 716 | new_plot.name = filename |
---|
[660b1e6] | 717 | new_plot.xaxis("\\rm{r}", 'A') |
---|
| 718 | new_plot.yaxis("\\rm{P(r)} ","cm^{-3}") |
---|
| 719 | |
---|
[f1181977] | 720 | # Store a ref to the plottable for later use |
---|
| 721 | self._added_plots[filename] = new_plot |
---|
| 722 | self._default_Iq[filename] = numpy.copy(y) |
---|
| 723 | |
---|
| 724 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title=filename)) |
---|
[660b1e6] | 725 | |
---|
| 726 | |
---|
[f3d51f6] | 727 | |
---|
| 728 | def start_thread(self): |
---|
| 729 | from pr_thread import CalcPr |
---|
| 730 | from copy import deepcopy |
---|
| 731 | |
---|
| 732 | # If a thread is already started, stop it |
---|
| 733 | if self.calc_thread != None and self.calc_thread.isrunning(): |
---|
| 734 | self.calc_thread.stop() |
---|
| 735 | |
---|
| 736 | pr = self.pr.clone() |
---|
| 737 | self.calc_thread = CalcPr(pr, self.nfunc, error_func=self._thread_error, completefn=self._completed, updatefn=None) |
---|
| 738 | self.calc_thread.queue() |
---|
| 739 | self.calc_thread.ready(2.5) |
---|
| 740 | |
---|
| 741 | def _thread_error(self, error): |
---|
| 742 | wx.PostEvent(self.parent, StatusEvent(status=error)) |
---|
| 743 | |
---|
[32dffae4] | 744 | def _estimate_completed(self, alpha, message, elapsed): |
---|
[f3d51f6] | 745 | """ |
---|
| 746 | Parameter estimation completed, |
---|
| 747 | display the results to the user |
---|
| 748 | @param alpha: estimated best alpha |
---|
| 749 | @param elapsed: computation time |
---|
| 750 | """ |
---|
| 751 | # Save useful info |
---|
| 752 | self.elapsed = elapsed |
---|
| 753 | self.control_panel.alpha_estimate = alpha |
---|
[32dffae4] | 754 | if not message==None: |
---|
| 755 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[35adaf6] | 756 | |
---|
| 757 | self.perform_estimateNT() |
---|
| 758 | |
---|
| 759 | |
---|
| 760 | |
---|
| 761 | def _estimateNT_completed(self, nterms, alpha, message, elapsed): |
---|
| 762 | """ |
---|
| 763 | Parameter estimation completed, |
---|
| 764 | display the results to the user |
---|
| 765 | @param alpha: estimated best alpha |
---|
| 766 | @param nterms: estimated number of terms |
---|
| 767 | @param elapsed: computation time |
---|
| 768 | """ |
---|
| 769 | # Save useful info |
---|
| 770 | self.elapsed = elapsed |
---|
| 771 | self.control_panel.nterms_estimate = nterms |
---|
| 772 | self.control_panel.alpha_estimate = alpha |
---|
| 773 | if not message==None: |
---|
| 774 | wx.PostEvent(self.parent, StatusEvent(status=str(message))) |
---|
[f3d51f6] | 775 | |
---|
| 776 | def _completed(self, out, cov, pr, elapsed): |
---|
| 777 | """ |
---|
| 778 | Method called with the results when the inversion |
---|
| 779 | is done |
---|
| 780 | |
---|
| 781 | @param out: output coefficient for the base functions |
---|
| 782 | @param cov: covariance matrix |
---|
| 783 | @param pr: Invertor instance |
---|
| 784 | @param elapsed: time spent computing |
---|
| 785 | """ |
---|
[dfb58f8] | 786 | from copy import deepcopy |
---|
[f3d51f6] | 787 | # Save useful info |
---|
| 788 | self.elapsed = elapsed |
---|
[feb21d8] | 789 | # Keep a copy of the last result |
---|
| 790 | self._last_pr = pr.clone() |
---|
| 791 | self._last_out = out |
---|
| 792 | self._last_cov = cov |
---|
| 793 | |
---|
[b659551] | 794 | # Save Pr invertor |
---|
| 795 | self.pr = pr |
---|
| 796 | |
---|
[d6113849] | 797 | #message = "Computation completed in %g seconds [chi2=%g]" % (elapsed, pr.chi2) |
---|
| 798 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 799 | |
---|
[dfb58f8] | 800 | cov = numpy.ascontiguousarray(cov) |
---|
| 801 | |
---|
[f3d51f6] | 802 | # Show result on control panel |
---|
| 803 | self.control_panel.chi2 = pr.chi2 |
---|
| 804 | self.control_panel.elapsed = elapsed |
---|
| 805 | self.control_panel.oscillation = pr.oscillations(out) |
---|
| 806 | #print "OSCILL", pr.oscillations(out) |
---|
[d6113849] | 807 | #print "PEAKS:", pr.get_peaks(out) |
---|
[dfb58f8] | 808 | self.control_panel.positive = pr.get_positive(out) |
---|
| 809 | self.control_panel.pos_err = pr.get_pos_err(out, cov) |
---|
[a4bd2ac] | 810 | self.control_panel.rg = pr.rg(out) |
---|
| 811 | self.control_panel.iq0 = pr.iq0(out) |
---|
| 812 | self.control_panel.bck = pr.background |
---|
[f3d51f6] | 813 | |
---|
[aa4b8379] | 814 | if False: |
---|
[0bae207] | 815 | for i in range(len(out)): |
---|
| 816 | try: |
---|
| 817 | print "%d: %g +- %g" % (i, out[i], math.sqrt(math.fabs(cov[i][i]))) |
---|
| 818 | except: |
---|
| 819 | print sys.exc_value |
---|
| 820 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 821 | |
---|
| 822 | # Make a plot of I(q) data |
---|
[aa4b8379] | 823 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 824 | new_plot.name = IQ_DATA_LABEL |
---|
[aa4b8379] | 825 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 826 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 827 | #new_plot.group_id = "test group" |
---|
| 828 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
[f3d51f6] | 829 | |
---|
| 830 | # Show I(q) fit |
---|
| 831 | self.show_iq(out, self.pr) |
---|
| 832 | |
---|
| 833 | # Show P(r) fit |
---|
[dfb58f8] | 834 | x_values, x_range = self.show_pr(out, self.pr, cov) |
---|
[f3d51f6] | 835 | |
---|
| 836 | # Popup result panel |
---|
| 837 | #result_panel = InversionResults(self.parent, -1, style=wx.RAISED_BORDER) |
---|
| 838 | |
---|
[2a92852] | 839 | def show_data(self, path=None, reset=False): |
---|
| 840 | """ |
---|
| 841 | Show data read from a file |
---|
| 842 | @param path: file path |
---|
| 843 | @param reset: if True all other plottables will be cleared |
---|
| 844 | """ |
---|
[0bae207] | 845 | if path is not None: |
---|
[ea5551f] | 846 | try: |
---|
| 847 | pr = self._create_file_pr(path) |
---|
[ceaf16e] | 848 | except: |
---|
| 849 | status="Problem reading data: %s" % sys.exc_value |
---|
| 850 | wx.PostEvent(self.parent, StatusEvent(status=status)) |
---|
| 851 | raise RuntimeError, status |
---|
[6f1f129] | 852 | |
---|
[ceaf16e] | 853 | # If the file contains nothing, just return |
---|
| 854 | if pr is None: |
---|
| 855 | raise RuntimeError, "Loaded data is invalid" |
---|
| 856 | |
---|
| 857 | self.pr = pr |
---|
[660b1e6] | 858 | |
---|
| 859 | # Make a plot of I(q) data |
---|
[357b79b] | 860 | if self.pr.err==None: |
---|
| 861 | new_plot = Theory1D(self.pr.x, self.pr.y) |
---|
| 862 | else: |
---|
| 863 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
[f1181977] | 864 | new_plot.name = IQ_DATA_LABEL |
---|
[660b1e6] | 865 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 866 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
[aa4b8379] | 867 | new_plot.interactive = True |
---|
[660b1e6] | 868 | #new_plot.group_id = "test group" |
---|
[2a92852] | 869 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="I(q)", reset=reset)) |
---|
[660b1e6] | 870 | |
---|
[0d88a09] | 871 | self.current_plottable = new_plot |
---|
| 872 | self.current_plottable.group_id = IQ_DATA_LABEL |
---|
| 873 | |
---|
| 874 | |
---|
[aa4b8379] | 875 | # Get Q range |
---|
| 876 | self.control_panel.q_min = self.pr.x.min() |
---|
| 877 | self.control_panel.q_max = self.pr.x.max() |
---|
| 878 | |
---|
[410aad8] | 879 | def save_data(self, filepath, prstate=None): |
---|
| 880 | """ |
---|
| 881 | Save data in provided state object. |
---|
| 882 | TODO: move the state code away from inversion_panel and move it here. |
---|
| 883 | Then remove the "prstate" input and make this method private. |
---|
| 884 | |
---|
| 885 | @param filepath: path of file to write to |
---|
| 886 | @param prstate: P(r) inversion state |
---|
| 887 | """ |
---|
| 888 | #TODO: do we need this or can we use DataLoader.loader.save directly? |
---|
| 889 | |
---|
| 890 | # Add output data and coefficients to state |
---|
| 891 | prstate.coefficients = self._last_out |
---|
| 892 | prstate.covariance = self._last_cov |
---|
| 893 | |
---|
| 894 | # Write the output to file |
---|
| 895 | self.state_reader.write(filepath, self.current_plottable, prstate) |
---|
| 896 | |
---|
[660b1e6] | 897 | |
---|
[2a92852] | 898 | def setup_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None, |
---|
| 899 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 900 | self.alpha = alpha |
---|
| 901 | self.nfunc = nfunc |
---|
| 902 | self.max_length = d_max |
---|
[634f1cf] | 903 | self.q_min = q_min |
---|
| 904 | self.q_max = q_max |
---|
[a4bd2ac] | 905 | self.has_bck = bck |
---|
[2a92852] | 906 | self.slit_height = height |
---|
| 907 | self.slit_width = width |
---|
[f3d51f6] | 908 | |
---|
[4a5de6f] | 909 | try: |
---|
[2a92852] | 910 | pr = self._create_plot_pr() |
---|
| 911 | if not pr==None: |
---|
| 912 | self.pr = pr |
---|
| 913 | self.perform_inversion() |
---|
[4a5de6f] | 914 | except: |
---|
| 915 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 916 | |
---|
[2a92852] | 917 | def estimate_plot_inversion(self, alpha, nfunc, d_max, q_min=None, q_max=None, |
---|
| 918 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 919 | self.alpha = alpha |
---|
| 920 | self.nfunc = nfunc |
---|
| 921 | self.max_length = d_max |
---|
[634f1cf] | 922 | self.q_min = q_min |
---|
| 923 | self.q_max = q_max |
---|
[a4bd2ac] | 924 | self.has_bck = bck |
---|
[2a92852] | 925 | self.slit_height = height |
---|
| 926 | self.slit_width = width |
---|
[f3d51f6] | 927 | |
---|
[4a5de6f] | 928 | try: |
---|
[2a92852] | 929 | pr = self._create_plot_pr() |
---|
| 930 | if not pr==None: |
---|
| 931 | self.pr = pr |
---|
| 932 | self.perform_estimate() |
---|
[4a5de6f] | 933 | except: |
---|
| 934 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 935 | |
---|
[2a92852] | 936 | def _create_plot_pr(self, estimate=False): |
---|
[f3d51f6] | 937 | """ |
---|
| 938 | Create and prepare invertor instance from |
---|
| 939 | a plottable data set. |
---|
| 940 | @param path: path of the file to read in |
---|
| 941 | """ |
---|
[ceaf16e] | 942 | # Sanity check |
---|
| 943 | if self.current_plottable is None: |
---|
| 944 | msg = "Please load a valid data set before proceeding." |
---|
| 945 | wx.PostEvent(self.parent, StatusEvent(status=msg)) |
---|
| 946 | return None |
---|
| 947 | |
---|
[f3d51f6] | 948 | # Get the data from the chosen data set and perform inversion |
---|
| 949 | pr = Invertor() |
---|
| 950 | pr.d_max = self.max_length |
---|
| 951 | pr.alpha = self.alpha |
---|
[634f1cf] | 952 | pr.q_min = self.q_min |
---|
| 953 | pr.q_max = self.q_max |
---|
[f3d51f6] | 954 | pr.x = self.current_plottable.x |
---|
| 955 | pr.y = self.current_plottable.y |
---|
[a4bd2ac] | 956 | pr.has_bck = self.has_bck |
---|
[2a92852] | 957 | pr.slit_height = self.slit_height |
---|
| 958 | pr.slit_width = self.slit_width |
---|
[f3d51f6] | 959 | |
---|
[d2ee6f6] | 960 | # Keep track of the plot window title to ensure that |
---|
| 961 | # we can overlay the plots |
---|
| 962 | if hasattr(self.current_plottable, "group_id"): |
---|
| 963 | pr.info["plot_group_id"] = self.current_plottable.group_id |
---|
| 964 | |
---|
[f3d51f6] | 965 | # Fill in errors if none were provided |
---|
[d2ee6f6] | 966 | err = self.current_plottable.dy |
---|
| 967 | all_zeros = True |
---|
| 968 | if err == None: |
---|
[d483799] | 969 | err = numpy.zeros(len(pr.y)) |
---|
[d2ee6f6] | 970 | else: |
---|
| 971 | for i in range(len(err)): |
---|
| 972 | if err[i]>0: |
---|
| 973 | all_zeros = False |
---|
| 974 | |
---|
| 975 | if all_zeros: |
---|
| 976 | scale = None |
---|
| 977 | min_err = 0.0 |
---|
[f3d51f6] | 978 | for i in range(len(pr.y)): |
---|
[d2ee6f6] | 979 | # Scale the error so that we can fit over several decades of Q |
---|
| 980 | if scale==None: |
---|
| 981 | scale = 0.05*math.sqrt(pr.y[i]) |
---|
| 982 | min_err = 0.01*pr.y[i] |
---|
| 983 | err[i] = scale*math.sqrt( math.fabs(pr.y[i]) ) + min_err |
---|
| 984 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 985 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
| 986 | |
---|
| 987 | pr.err = err |
---|
[2a92852] | 988 | |
---|
| 989 | return pr |
---|
[f3d51f6] | 990 | |
---|
| 991 | |
---|
[2a92852] | 992 | def setup_file_inversion(self, alpha, nfunc, d_max, path, q_min=None, q_max=None, |
---|
| 993 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 994 | self.alpha = alpha |
---|
| 995 | self.nfunc = nfunc |
---|
| 996 | self.max_length = d_max |
---|
[634f1cf] | 997 | self.q_min = q_min |
---|
| 998 | self.q_max = q_max |
---|
[a4bd2ac] | 999 | self.has_bck = bck |
---|
[2a92852] | 1000 | self.slit_height = height |
---|
| 1001 | self.slit_width = width |
---|
[f3d51f6] | 1002 | |
---|
[4a5de6f] | 1003 | try: |
---|
[2a92852] | 1004 | pr = self._create_file_pr(path) |
---|
| 1005 | if not pr==None: |
---|
| 1006 | self.pr = pr |
---|
[4a5de6f] | 1007 | self.perform_inversion() |
---|
| 1008 | except: |
---|
| 1009 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
[f3d51f6] | 1010 | |
---|
[2a92852] | 1011 | def estimate_file_inversion(self, alpha, nfunc, d_max, path, q_min=None, q_max=None, |
---|
| 1012 | bck=False, height=0, width=0): |
---|
[f3d51f6] | 1013 | self.alpha = alpha |
---|
| 1014 | self.nfunc = nfunc |
---|
| 1015 | self.max_length = d_max |
---|
[634f1cf] | 1016 | self.q_min = q_min |
---|
| 1017 | self.q_max = q_max |
---|
[a4bd2ac] | 1018 | self.has_bck = bck |
---|
[2a92852] | 1019 | self.slit_height = height |
---|
| 1020 | self.slit_width = width |
---|
[f3d51f6] | 1021 | |
---|
[4a5de6f] | 1022 | try: |
---|
[2a92852] | 1023 | pr = self._create_file_pr(path) |
---|
| 1024 | if not pr==None: |
---|
| 1025 | self.pr = pr |
---|
[4a5de6f] | 1026 | self.perform_estimate() |
---|
| 1027 | except: |
---|
| 1028 | wx.PostEvent(self.parent, StatusEvent(status=sys.exc_value)) |
---|
| 1029 | |
---|
[f3d51f6] | 1030 | |
---|
| 1031 | def _create_file_pr(self, path): |
---|
| 1032 | """ |
---|
| 1033 | Create and prepare invertor instance from |
---|
| 1034 | a file data set. |
---|
| 1035 | @param path: path of the file to read in |
---|
| 1036 | """ |
---|
| 1037 | # Load data |
---|
| 1038 | if os.path.isfile(path): |
---|
[357b79b] | 1039 | |
---|
[0bae207] | 1040 | if self._current_file_data is not None \ |
---|
| 1041 | and self._current_file_data.path==path: |
---|
[aab8ad7] | 1042 | # Protect against corrupted data from |
---|
| 1043 | # previous failed load attempt |
---|
| 1044 | if self._current_file_data.x is None: |
---|
| 1045 | return None |
---|
[0bae207] | 1046 | x = self._current_file_data.x |
---|
| 1047 | y = self._current_file_data.y |
---|
| 1048 | err = self._current_file_data.err |
---|
[d7412e0] | 1049 | |
---|
| 1050 | message = "The data from this file has already been loaded." |
---|
| 1051 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[0bae207] | 1052 | else: |
---|
[e43c012] | 1053 | # Reset the status bar so that we don't get mixed up |
---|
| 1054 | # with old messages. |
---|
| 1055 | #TODO: refactor this into a proper status handling |
---|
| 1056 | wx.PostEvent(self.parent, StatusEvent(status='')) |
---|
[ceaf16e] | 1057 | try: |
---|
| 1058 | x, y, err = self.load(path) |
---|
| 1059 | except: |
---|
[d7412e0] | 1060 | load_error(sys.exc_value) |
---|
[ceaf16e] | 1061 | return None |
---|
[6f1f129] | 1062 | |
---|
| 1063 | # If the file contains no data, just return |
---|
[d7412e0] | 1064 | if x is None or len(x)==0: |
---|
| 1065 | load_error("The loaded file contains no data") |
---|
[6f1f129] | 1066 | return None |
---|
[357b79b] | 1067 | |
---|
| 1068 | # If we have not errors, add statistical errors |
---|
[aab8ad7] | 1069 | if err==None and y is not None: |
---|
[357b79b] | 1070 | err = numpy.zeros(len(y)) |
---|
[aab8ad7] | 1071 | scale = None |
---|
| 1072 | min_err = 0.0 |
---|
[357b79b] | 1073 | for i in range(len(y)): |
---|
[aab8ad7] | 1074 | # Scale the error so that we can fit over several decades of Q |
---|
| 1075 | if scale==None: |
---|
| 1076 | scale = 0.05*math.sqrt(y[i]) |
---|
| 1077 | min_err = 0.01*y[i] |
---|
| 1078 | err[i] = scale*math.sqrt( math.fabs(y[i]) ) + min_err |
---|
[357b79b] | 1079 | message = "The loaded file had no error bars, statistical errors are assumed." |
---|
| 1080 | wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 1081 | |
---|
[aab8ad7] | 1082 | try: |
---|
| 1083 | # Get the data from the chosen data set and perform inversion |
---|
| 1084 | pr = Invertor() |
---|
| 1085 | pr.d_max = self.max_length |
---|
| 1086 | pr.alpha = self.alpha |
---|
| 1087 | pr.q_min = self.q_min |
---|
| 1088 | pr.q_max = self.q_max |
---|
| 1089 | pr.x = x |
---|
| 1090 | pr.y = y |
---|
| 1091 | pr.err = err |
---|
| 1092 | pr.has_bck = self.has_bck |
---|
| 1093 | pr.slit_height = self.slit_height |
---|
| 1094 | pr.slit_width = self.slit_width |
---|
| 1095 | return pr |
---|
| 1096 | except: |
---|
[d7412e0] | 1097 | load_error(sys.exc_value) |
---|
[2a92852] | 1098 | return None |
---|
[f3d51f6] | 1099 | |
---|
| 1100 | def perform_estimate(self): |
---|
| 1101 | from pr_thread import EstimatePr |
---|
| 1102 | from copy import deepcopy |
---|
| 1103 | |
---|
| 1104 | # If a thread is already started, stop it |
---|
| 1105 | if self.estimation_thread != None and self.estimation_thread.isrunning(): |
---|
| 1106 | self.estimation_thread.stop() |
---|
| 1107 | |
---|
| 1108 | pr = self.pr.clone() |
---|
| 1109 | self.estimation_thread = EstimatePr(pr, self.nfunc, error_func=self._thread_error, |
---|
| 1110 | completefn = self._estimate_completed, |
---|
| 1111 | updatefn = None) |
---|
| 1112 | self.estimation_thread.queue() |
---|
| 1113 | self.estimation_thread.ready(2.5) |
---|
[35adaf6] | 1114 | |
---|
| 1115 | def perform_estimateNT(self): |
---|
| 1116 | from pr_thread import EstimateNT |
---|
| 1117 | from copy import deepcopy |
---|
| 1118 | |
---|
| 1119 | # If a thread is already started, stop it |
---|
| 1120 | if self.estimation_thread != None and self.estimation_thread.isrunning(): |
---|
| 1121 | self.estimation_thread.stop() |
---|
| 1122 | |
---|
| 1123 | pr = self.pr.clone() |
---|
[2a92852] | 1124 | # Skip the slit settings for the estimation |
---|
| 1125 | # It slows down the application and it doesn't change the estimates |
---|
| 1126 | pr.slit_height = 0.0 |
---|
| 1127 | pr.slit_width = 0.0 |
---|
[35adaf6] | 1128 | self.estimation_thread = EstimateNT(pr, self.nfunc, error_func=self._thread_error, |
---|
| 1129 | completefn = self._estimateNT_completed, |
---|
| 1130 | updatefn = None) |
---|
| 1131 | self.estimation_thread.queue() |
---|
| 1132 | self.estimation_thread.ready(2.5) |
---|
[f3d51f6] | 1133 | |
---|
| 1134 | def perform_inversion(self): |
---|
| 1135 | |
---|
| 1136 | # Time estimate |
---|
| 1137 | #estimated = self.elapsed*self.nfunc**2 |
---|
[2a92852] | 1138 | #message = "Computation time may take up to %g seconds" % self.elapsed |
---|
| 1139 | #wx.PostEvent(self.parent, StatusEvent(status=message)) |
---|
[f3d51f6] | 1140 | |
---|
| 1141 | # Start inversion thread |
---|
| 1142 | self.start_thread() |
---|
| 1143 | return |
---|
| 1144 | |
---|
| 1145 | out, cov = self.pr.lstsq(self.nfunc) |
---|
| 1146 | |
---|
| 1147 | # Save useful info |
---|
| 1148 | self.elapsed = self.pr.elapsed |
---|
| 1149 | |
---|
| 1150 | for i in range(len(out)): |
---|
| 1151 | try: |
---|
| 1152 | print "%d: %g +- %g" % (i, out[i], math.sqrt(math.fabs(cov[i][i]))) |
---|
| 1153 | except: |
---|
| 1154 | print "%d: %g +- ?" % (i, out[i]) |
---|
| 1155 | |
---|
| 1156 | |
---|
| 1157 | |
---|
| 1158 | # Make a plot of I(q) data |
---|
| 1159 | new_plot = Data1D(self.pr.x, self.pr.y, dy=self.pr.err) |
---|
| 1160 | new_plot.name = "I_{obs}(q)" |
---|
| 1161 | new_plot.xaxis("\\rm{Q}", 'A^{-1}') |
---|
| 1162 | new_plot.yaxis("\\rm{Intensity} ","cm^{-1}") |
---|
| 1163 | wx.PostEvent(self.parent, NewPlotEvent(plot=new_plot, title="Iq")) |
---|
| 1164 | |
---|
| 1165 | # Show I(q) fit |
---|
| 1166 | self.show_iq(out, self.pr) |
---|
| 1167 | |
---|
| 1168 | # Show P(r) fit |
---|
| 1169 | x_values, x_range = self.show_pr(out, self.pr, cov=cov) |
---|
| 1170 | |
---|
| 1171 | |
---|
| 1172 | |
---|
| 1173 | def _on_context_inversion(self, event): |
---|
| 1174 | panel = event.GetEventObject() |
---|
| 1175 | |
---|
| 1176 | # If we have more than one displayed plot, make the user choose |
---|
[aa4b8379] | 1177 | if len(panel.plots)>1 and panel.graph.selected_plottable in panel.plots: |
---|
| 1178 | dataset = panel.graph.selected_plottable |
---|
[f3d51f6] | 1179 | elif len(panel.plots)==1: |
---|
| 1180 | dataset = panel.plots.keys()[0] |
---|
| 1181 | else: |
---|
| 1182 | print "Error: No data is available" |
---|
| 1183 | return |
---|
| 1184 | |
---|
| 1185 | # Store a reference to the current plottable |
---|
[3fd1ebc] | 1186 | # If we have a suggested value, use it. |
---|
| 1187 | try: |
---|
| 1188 | estimate = float(self.control_panel.alpha_estimate) |
---|
| 1189 | self.control_panel.alpha = estimate |
---|
| 1190 | except: |
---|
| 1191 | self.control_panel.alpha = self.alpha |
---|
| 1192 | print "No estimate yet" |
---|
| 1193 | pass |
---|
[d6113849] | 1194 | try: |
---|
| 1195 | estimate = int(self.control_panel.nterms_estimate) |
---|
| 1196 | self.control_panel.nfunc = estimate |
---|
| 1197 | except: |
---|
| 1198 | self.control_panel.nfunc = self.nfunc |
---|
| 1199 | print "No estimate yet" |
---|
| 1200 | pass |
---|
[3fd1ebc] | 1201 | |
---|
[f3d51f6] | 1202 | self.current_plottable = panel.plots[dataset] |
---|
| 1203 | self.control_panel.plotname = dataset |
---|
[d6113849] | 1204 | #self.control_panel.nfunc = self.nfunc |
---|
[f3d51f6] | 1205 | self.control_panel.d_max = self.max_length |
---|
| 1206 | self.parent.set_perspective(self.perspective) |
---|
[aa4b8379] | 1207 | self.control_panel._on_invert(None) |
---|
[f3d51f6] | 1208 | |
---|
| 1209 | def get_panels(self, parent): |
---|
| 1210 | """ |
---|
| 1211 | Create and return a list of panel objects |
---|
| 1212 | """ |
---|
| 1213 | from inversion_panel import InversionControl |
---|
| 1214 | |
---|
| 1215 | self.parent = parent |
---|
[aa4b8379] | 1216 | self.control_panel = InversionControl(self.parent, -1, |
---|
| 1217 | style=wx.RAISED_BORDER, |
---|
| 1218 | standalone=self.standalone) |
---|
[f3d51f6] | 1219 | self.control_panel.set_manager(self) |
---|
| 1220 | self.control_panel.nfunc = self.nfunc |
---|
| 1221 | self.control_panel.d_max = self.max_length |
---|
| 1222 | self.control_panel.alpha = self.alpha |
---|
| 1223 | |
---|
| 1224 | self.perspective = [] |
---|
| 1225 | self.perspective.append(self.control_panel.window_name) |
---|
[aa4b8379] | 1226 | |
---|
| 1227 | self.parent.Bind(EVT_PR_FILE, self._on_new_file) |
---|
| 1228 | |
---|
[f3d51f6] | 1229 | return [self.control_panel] |
---|
| 1230 | |
---|
[aa4b8379] | 1231 | def _on_new_file(self, evt): |
---|
| 1232 | """ |
---|
| 1233 | Called when the application manager posted an |
---|
| 1234 | EVT_PR_FILE event. Just prompt the control |
---|
| 1235 | panel to load a new data file. |
---|
| 1236 | """ |
---|
| 1237 | self.control_panel._change_file(None) |
---|
| 1238 | |
---|
[f3d51f6] | 1239 | def get_perspective(self): |
---|
| 1240 | """ |
---|
| 1241 | Get the list of panel names for this perspective |
---|
| 1242 | """ |
---|
| 1243 | return self.perspective |
---|
| 1244 | |
---|
| 1245 | def on_perspective(self, event): |
---|
| 1246 | """ |
---|
| 1247 | Call back function for the perspective menu item. |
---|
| 1248 | We notify the parent window that the perspective |
---|
| 1249 | has changed. |
---|
| 1250 | """ |
---|
| 1251 | self.parent.set_perspective(self.perspective) |
---|
| 1252 | |
---|
| 1253 | def post_init(self): |
---|
| 1254 | """ |
---|
| 1255 | Post initialization call back to close the loose ends |
---|
| 1256 | [Somehow openGL needs this call] |
---|
| 1257 | """ |
---|
[d2ee6f6] | 1258 | if self.standalone==True: |
---|
| 1259 | self.parent.set_perspective(self.perspective) |
---|
[35adaf6] | 1260 | |
---|
| 1261 | if __name__ == "__main__": |
---|
| 1262 | i = Plugin() |
---|
| 1263 | print i.perform_estimateNT() |
---|
| 1264 | |
---|
| 1265 | |
---|
| 1266 | |
---|
[660b1e6] | 1267 | |
---|